There does appear to be a problem with environment variable expansion when set within the Properties-->Application-->Environment section.
I will create a bug report for that. If you would like to open a new support incident and reference my name in the description I will ensure that the bug report is added to your incident so that you will be notified when it is fixed.
As a workaround you could add an application.config file to the project and set the environment variables there. These appear to expand correctly. When setting them within application.config they will be set both when running the application within the IDE and outside of it.
Thanks